Interpretive Summary: Chickpea is an economically important crop worldwide, especially in developing countries where it serves as a staple dietary source of protein. Chickpea germplasm enhancement is a major objective of breeding programs which are using genomics approaches to identify superior genotypes. Development of linkage maps for the chickpea genome has generated greater understanding of the genome. Early maps were based primarily on random markers while more recent maps include sequence based markers. Development of bacterial artificial chromosome and cDNA libraries has also provided additional tools for chickpea genome analysis. Despite these advancements, absence of polymorphism within chickpea remains a significant barrier to placing many genes on the genetic map and identifying useful markers. Single nucleotide polymorphisms (SNPs) are reported to be abundant in plant genomes and identification of SNPs in chickpea offer additional methods to develop new markers for genome mapping. Application of marker systems based on SNPs such as cleaved amplified polymorphic sequence and derived cleaved amplified polymorphic sequence in chickpea mapping where absence of polymorphism is a constraint is expected to improve generation of high density maps necessary for map-based cloning and integration of physical and genetic maps.

Technical Abstract:
Cleaved amplified polymorphic sequence (CAPS) and derived cleaved amplified polymorphic sequence markers (dCAPS) are sequence based and co-dominant markers. Primers were designed from the ends of bacterial artificial chromosome clones 4m10 and 15o9 as well as a partial sequence of aldolase using Primer3. Amplified products were cloned into the pGEM-T Easy vector and sequenced on an ABI Prism 377 DNA sequencer using the dideoxy sequencing method and T7 universal primer. Sequence from parental DNA samples were compared using Vector NTI Advance 9.0 software for SNP detection and restriction mapping. SNPs resulting in differential restriction enzyme sites between the parental sequence were used to develop CAPS and dCAPS assays. Application of CAPS and dCAPS in chickpea mapping where absence of polymorphism is a constraint is expected to improve generation of high density maps necessary for map-based cloning and integration of physical and genetic maps.